Fragmentation reactions of protonated α,ω‐diamino carboxylic acids: The importance of functional group interactions
Bibliographic record
Abstract
Abstract Protonated members of a homologous series of biologically significant α,ω‐diamino carboxylic acids were subjected to collision induced dissociation (CID). The resulting fragmentation patterns were studied using isotopic labeling, quantum mechanical computations, and pseudo MS 3 experiments conducted primarily on an ion trap mass spectrometer. Each protonated α,ω‐diamino acid showed a primary neutral loss of either ammonia or water; a clear explanation was developed for the observed variation of the two losses within the series. Protonated 2,3‐diaminopropanoic acid, 2,4‐diaminobutanoic acid, and 2,7‐diaminoheptanoic acid gave secondary losses of water, carbon monoxide, and a loss of water plus carbon monoxide, respectively. In the parallel pathways characterized for the fragmentations of protonated ornithine and lysine, the α‐nitrogen of the diamino acid was maintained in the cyclic iminium product formed by successive losses of NH 3 and (H 2 O + CO), whereas the side‐chain nitrogen was retained by consecutive losses of H 2 O and (CO, NH 3 ). The 1‐piperideine ion from protonated lysine was fragmented further, losing ethylene from carbons 4 and 5. Protonated 2,6‐diaminopimelic acid fragmented by analogous reactions. Detailed mechanistic schemes for the fragmentation of both protonated 2,3‐diaminopropanoic and ornithine were generated from MP2/DFT computations. This work highlights the participation of the side‐chain amino group, which distinguishes the gas‐phase chemistry of protonated α,ω‐diamino acids from the well‐documented fragmentation reactions of protonated α‐amino acids bearing a hydrogen atom or an alkyl side chain. In general, the results further illustrate the importance of intramolecular separations affecting the specific interactions between functional groups leading to the fragmentation of multifunctional ions.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.010 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".